Re: [Freesurfer] FsFast Functional Connectivity with subject-specific surface seeds

Hi Lingqiang, I did not have a strong reason not to do the low pass filtering. I think I tried it once and it did not seem to make much difference, so I did not implement it in FSFAST. The differences may be due to filtering, but there are a lot of other places where things can be different too

[Freesurfer] Talairach transform issue; V 5.0

Hello Freesurfer Experts- We recently reran several subjects from scratch through the stable Freesurfer 5.0 pipeline who had previously been processed with the stable 4.5 pipeline. We used tkregister2 for QA of the 5.0 data and noticed that the talairach transform was off (misaligned) for th

Re: [Freesurfer] FsFast Functional Connectivity with subject-specific surface seeds

Thanks Doug. The labels work perfectly now. I also have a methodological question about the fsfast connectivity analysis: functional connectivity analyses in the literature (Biswal, etc) only looks at low-frequency fluctuations from BOLD signals. After preprocessing and regressing out nuisance re

[Freesurfer] Tracula - bedpost failure

Hi Everyone -- I've been having difficulty getting Tracula to run smoothly on our cluster. Similar to others on the listserv, the bedpost step was not creating the necessary files causing an error during the -path step. Based on previous posts, I ran bedpostx on the dmri directory. This initially

Re: [Freesurfer] mri_matrix_multiply to move functional images to common space

When you run your original mri_vol2vol command, add --reg-final reg.final.dat. You can then use mri_vol2vol --reg reg.final.dat --mov yourmovvol.nii --targ yourvolume.mni305.nii --inv --o new.yourmovvol.nii to map it back to the moveable space doug Andrew Dumas wrote: > Thanks, Doug! One mor

Re: [Freesurfer] mri_matrix_multiply to move functional images to common space

Yea, you need to do it in the two steps you mention. You can do that from one command line with something like bbregister --s subject --mov epi.nii --init-{fsl,header} --bold --int aascout.nii --o register.dat The --int is an "intermediate" volume. doug Andrew Dumas wrote: > That did the trick,

Re: [Freesurfer] labels broblem

I don't think so. If you use version 5.1, it will generate the 2009 labels. doug LAOUCHEDI MAKHLOUF wrote: > hi everyone > i run recon-all -all on some subjects using the 5.1 > version of freesurfer and instead of getting aparc.a2009s+aseg.mgz i > got aparc.a2005s+aseg.mgz. the

Re: [Freesurfer] mri_glmfit-sim error

Hi Joost, the precomputed tables only go up to 30mm FWHM. The 25 mm you apply adds to some that is already there to cause it to be 31mm, so the table does not exist. I would say that 25mm is a lot to smooth by. Do you really need that much? doug j janssen wrote: > Hi, > > - FS version: 5.1 > -

Re: [Freesurfer] mri_matrix_multiply to move functional images to common space

Thanks, Doug! One more question-- How can I invert this registration? I want to move the volumes in the common space back to each original subject space. mri_vol2vol won't accept a --targ when I specify --tal, but I'd like to use --inv. Andrew On Tue, 2011-12-20 at 14:58 -0500, Douglas N Greve wr

Re: [Freesurfer] Error with mri_cvs_register

Hi Antonella, Can you send the log file so that we can figure out where your process stopped? Lilla On Thu, 22 Dec 2011, Antonella Kis wrote: > Dear experts, > > I was running the mri_cvs_register for a few times for a subject and I am > getting an error. The registration will not bwe compl

[Freesurfer] Error with mri_cvs_register

Dear experts, I was running the mri_cvs_register for a few times for a subject and I am getting an error. The registration will not bwe completed but I got most of the files so I wonder if I need to re-run the whole registration steps or there is a way to just re-run the registration from the s

[Freesurfer] labels broblem

hi everyone   i run recon-all -all on some subjects using the 5.1 version of freesurfer and instead of getting aparc.a2009s+aseg.mgz i got aparc.a2005s+aseg.mgz. the components of the cingulate cortex are quite different in both files a2005s and a2009s : in a2009s i used in my w

[Freesurfer] Fwd: Reading annotation file in Matlab

Hmm, found the problem. These two labels represent 'non-cortex' areas and are therefore zero. They where however wrongly mapped further in my script. Conclusion: everything works as it should work. :-). -- Forwarded message -- From: Martijn Steenwijk Date: Thu, Dec 22, 2011 at 1:

Re: [Freesurfer] Reading annotation file in Matlab

You are right. I found out the same using the wiki http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles. However, I discovered that read_annotation.m reads some labels as zeros and 'misses' labels 1639705 and 3294840 defined in the enclosed LUT while reading for example lh.aparc.anno

Re: [Freesurfer] Reading annotation file in Matlab

Hi, I am not sure if your question is about read_annotation or aparc.annot in particular. read_annotation.m reads the labels embedded in the annotation file you passed to it. The labels embedded in the annotation file may or may not be the same as those in FreeSurferColorLUT. I could be wrong, bu

Re: [Freesurfer] Selxavg3 sets high activation to zero

Ok, that's great. Thanks very much for your help. Best wishes and Merry Christmas! Qi Zhu, PostDoc Laboratorium voor Neuro- en Psychofysiologie K.U.Leuven Medical School Herestraat 49, B-3000 Leuven (Belgium) On Wed, Dec 21, 2011 at 7:40 PM, Douglas N Greve wrote: > Yes that is correct. That wa

[Freesurfer] Reading annotation file in Matlab

Dear all, I'm trying to read aparc.annot into Matlab using the matlab/read_annotation.m function. Is it correct that the *labels* read by this function do not correspond with for example the FreeSurferColorLUT? Are the labels stored as 16 bit (unsigned)integers, or in another way? Best, Martijn